Do not assume anything.
Start again testing all the basics. . . .
Compression test and leak-down test.
Check the charging system, battery and terminal connections.
check the fuel system has the correct fuel delivery quantity over given time, (be sure pump can deliver X amount of litres over X amount of time, the correct figures for this is in the service manual)
Test all the coils on a coil tester.
Check all the connections at the coils and voltage at the coil connectors.
Test the sensors as in the service manual.
Sort the airbox and seal it as it should be.
Basics. Systematic checks are the way to go rather than stabbing in the dark and working on a 'hunch'.
Let us know how it works out, pics and a decent description of the symptoms always helps too !